Question: WGCNA : Module trait relationships
2
gravatar for msumaira36
3.3 years ago by
msumaira3620
msumaira3620 wrote:

I am applying wgcna on my data set. My data set contains 20 samples. Out of these 20 samples, 10 are of smokers and 10 are of nonsmokers. 10 samples for each smokers and non- smokers are further divided into 5 samples from cancer patients and 5 from normal. The data is obtained from rna-seq platform. Raw counts are normalized by using vst normalization and quantile normalization. WGCNA has resulted in 29 modules. Problem i am facing is in trait module relation ship heatmap. I want to get modules that are highly correlated with cancer, smokers and non smokers. These three variables are taken as traits in trait file. The problem is that no module is significantly correlated with any trait. P-values are very large like 0.2, 0.4 etc.

Please help me finding what am i doing wrong?? Why there is no significance module ? Is that some problem of data normalization ?

Thankyou in advance..

wgcna • 2.2k views
ADD COMMENTlink modified 13 months ago by Kevin Blighe61k • written 3.3 years ago by msumaira3620

may there are no significant result at all ,what is the number of genes you have ? did you use some filter before going into WGCNA

ADD REPLYlink written 24 months ago by krushnach80810
3
gravatar for Kevin Blighe
13 months ago by
Kevin Blighe61k
University College London
Kevin Blighe61k wrote:

This is nothing out of the ordinary. Please read the words of the WGCNA developer: https://support.bioconductor.org/p/116420/#116422

Kevin

ADD COMMENTlink written 13 months ago by Kevin Blighe61k
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